Characterization of Loss-of-Imprinting in Breast Cancer at the Cellular Level by Integrating Single-Cell Full-Length Transcriptome with Bulk RNA-Seq Data.

ABSTRACT: Genomic imprinting, the parent-of-origin-specific gene expression, plays a pivotal role in growth regulation and is often dysregulated in cancer. However, screening for imprinting is complicated by its cell-type specificity, which bulk RNA-seq cannot capture. On the other hand, large-scale single-cell RNA-seq (scRNA-seq) often lacks transcript-level detail and is cost-prohibitive. Here, we address this gap by integrating bulk RNA-seq with full-length transcript scRNA-seq to investigate imprinting dynamics in breast cancer. By analyzing scRNA-seq data from 486 cancer cells across subtypes, we identified multiple SNPs in imprinted genes, including HM13, MEST (PEG1), SNHG14 and PEG10, showing consistent biallelic expression. Bulk RNA-seq, however, revealed t

SUBMITTER: Amin MT 

PROVIDER: S-EPMC11673884 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature